1. Chap.2 Basic concepts of Biology

2. 5 basic groups of microbes a. bacteria Bacteria are typically unicellular, microscopic, prokaryotic organisms that reproduce by bi nary fission (see Fig. 1 and Fig.2).Fig. 1Fig.2 b. fungi: yeasts and molds Yeasts are typically unicellular, microscopic, eukaryotic fungi that reproduce asexually by budding (see Fig. 3 and Fig. 4).Fig. 3Fig. 4 Molds are typically filamentous, eukaryotic fungi that reproduce by producing asexual rep roductive spores (see Fig. 5 and Fig. 6)Fig. 5Fig. 6 c. viruses Viruses are typically submicroscopic, acellular infectious particles that can only replicate i nside a living host cell. The vast majority of viruses possess either DNA or RNA but not bot h (see Fig. 7 and Fig. 8).Fig. 7Fig. 8 d. protozoa Protozoa are typically unicellular, microscopic, eukaryotic organisms that lack a cell wall ( see Fig. 9 and Fig. 10).Fig. 9Fig. 10 e. algae Algae are typically eukaryotic microorganisms that carry out photosynthesis (see Fig 11 an d Fig. 12).Fig 11Fig. 12

3. Terms -phil- (-phile, -philia, -philic) are used to spe cify some kind of attraction or affinity to somethi ng, in particular the love or obsession with some thing. They are antonymic to suffixes -phob-.antonymic-phob- Phil- (Philo-) may also be used as a prefix with a similar meaning.

4. Microorganism -temperature mesophilia / mesophile: Preference of moderate temperatures in microorganisms.mesophiliamesophile psychrophilia / psychrophile: Preference of cold temperatures.psychrophiliapsychrophile thermophilia: Love of high temperatures; thrivin g in high temperatures (e.g. microbes).thermophilia

5. microorganism Biology acidophilia / acidophile: Preference of acidic conditionsacidophiliaacidophile alkaliphilia / alkaliphile: Preference of alkaline environments.alkaliphiliaalkaliphile anthophilia / anthophile / anthophilic: Attraction to flowers.anthophiliaanthophileanthophilic anthrophile / anthrophilic: Attracted to humans (e.g., parasites).anthrophileanthrophilic anemophily: a form of pollination whereby pollen is distributed by wind.anemophily cryophilia / cryophilic / cryophile: Preference for cold environments, climates, objects and l ow temperatures; e.g., Protea cryophila (Snow Protea).cryophiliacryophiliccryophileProtea cryophila extremophilia / extremophile: Preference of living extremal conditions for some microorga nisms.extremophiliaextremophile geophilia / geophilic / Geophile Referring to organisms that prefer the soil.geophiliageophilicGeophile halophilia / halophile: Attraction/attracted to salt or salt-water.halophiliahalophile heliophilia / heliophile: Attraction/attracted to sunlight.heliophiliaheliophile hydrophilia: Attraction to water.hydrophilia hyperthermophilia / hyperthermophile / hyperthermophilic: Describing organisms that thr ive in extremely hot environments.hyperthermophiliahyperthermophilehyperthermophilic limnophilia / limnophile / limnophilic: Preference of ponds or marshes.limnophilialimnophilelimnophilic lithophilia / lithophile / litophilic: Preference/affinity to stones.lithophilialithophilelitophilic

6. microorganism microaerophilia / microaerophile / Microaerophilic: of organisms that can tolerate or requi re environments containing low levels of oxygen.microaerophiliamicroaerophileMicroaerophilic myrmecophilia: in names of orchids of genus myrmecophila, "love of ants"myrmecophiliaorchidsmyrmecophila nemophilia: Love of the woods/forests, in the name of the genus Nemophilia of flowers.nemophiliaNemophiliaflowers nyctophilia: A preference for darkness or night. ombrophilia / ombrophile: Affinity/affined to large amounts of rainfall.ombrophiliaombrophile petrophilia / petrophile / petrophilic: Preference of living or spending time in rocky areas.petrophiliapetrophilepetrophilic photophilia / photophile / photophilic: Preference of living or spending time in lighted con ditions.photophiliaphotophilephotophilic psammophile: A plant loving sandy areas (psammophyte).psammophilepsammophyte rheophilia: Preference of living in running water.rheophilia rhizophilia: Preference of living on roots.rhizophilia tropophilia / tropophile / tropophilous: Preference of seasonal extremes of climate.tropophiliatropophiletropophilous xerophilia: Love of living or spending time in very dry conditions.xerophilia xylophilia: Love of wood.xylophilia zoophily: a form of pollination whereby pollen is distributed by animals.zoophily

7. Introduction to bacteria -Morphology and classification Bacillus (plural, bacilli): rod- like Coccus (plural, cocci): spherical -cocci often take on multi-cell forms: =two cocci: diplococci =chains of cocci: streptococci

8. 1. The coccus The cocci are spherical or oval bacteria having one of several distinct arrang ements based on their planes of division.arrang ements a. Division in one plane produces either a diplococcus or streptococcu s arrangement. b. Division in two planes produces a tetrad arrangement. a tetrad: cocci arranged in squares of 4 - photomicrograph of a tetradtetrad c. Division in three planes produces a sarcina arrangement. sarcina: cocci in arranged cubes of 8 - photomicrograph of a sarcinasarcina d. Division in random planes produces a staphylococcus arrangement. staphylococcus: cocci arranged in irregular, often grape-like clusters - photomicrograph of a staphylococcus An average coccus is about 0.5-1.0 micrometer (µm) in diameter. (A micro meter equals 1/1,000,000 of a meter.)staphylococcus

9. 2. The rod or bacillus Bacilli are rod-shaped bacteria. Bacilli all divide in o ne plane producing a bacillus, streptobacillus, or coccobacillus arrangement.arrangement a. bacillus: single bacilli -(eg., Escherichia coli O157H7, a bacillus)Escherichia coli O157H7, a bacillus b. streptobacillus: bacilli arranged in chains - photomicrograph of a streptobacillusstreptobacillus c. coccobacillus: oval and similar to a coccus An average bacillus is 0.5-1.0 µm wide by 1.0-4.0 µm long.

10. 3. The spiral Spirals come in one of three forms, a vibrio, a spiri llum, or a spirochete.forms a. vibrio: a curved or comma-shaped rod - photomicrograph of a vibriovibrio b. spirillum: a thick, rigid spiral - photomicrograph of a spirillumspirillum c. spirochete: a thin, flexible spiral - photomicrograph of a spirochetespirochete Spirals range in size from 1 µm to over 100 µm in len gth.

11. 1. nuclear body eukaryotic cell a. The nuclear body is bounde d by a nuclear membrane havi ng pores connecting it with the endoplasmic reticulum b. It contains one or more pair ed, linear chromosomes comp osed of deoxyribonucleic acid ( DNA) associated with histone proteins. c. A nucleolus is present. d. The nuclear body is called a nucleus prokaryotic cell a. The nuclear body is not bou nded by a nuclear membrane. b. It usually contains one circu lar chromosome composed of deoxyribonucleic acid (DNA) a ssociated with histone-like pro teins. c. There is no nucleolus. d. The nuclear body is called a nucleoid

12. 2. cell division eukaryotic cell a. The nucleus divides by mito sis. b. Haploid (1N) sex cells in dip loid or 2N organisms are prod uced through meiosis prokaryotic cell a. The cell usually divides by bin ary fission. There is no mitosis. b. Prokaryotic cells are haploid. Meiosis is not needed.

13. 3. cytoplasmic membrane - also known as a cell membrane or plasma me mbrane eukaryotic cell a. The cytoplasmic membrane is a fluid phospholipid bilayer containing sterols. b. The membrane is capable of endocytosis (phagocytosis and pinocytosis) and exocytosis.sterols prokaryotic cell a. The cytoplasmic membrane; is a fluid phospholipid bilayer usually lacking sterols. Many bacteria do contain stero l-like molecules called hopanoi ds.hopanoi ds b.The membrane is incapable of endocytosis and exocytosis

14. 4. cytoplasmic structures eukaryotic cell a. The ribosomes are composed of a 60 S and a 40S subunit forming an 80S ri bosome. b. Internal membrane-bound organell es such as mitochondria, endoplasmic reticulum, Golgi apparatus, vacuoles, and lysosomes are present. c. Chloroplasts serve as organelles for photosynthesis. d. A mitotic spindle involved in mitosi s is present during cell division. e. A cytoskeleton is present. It contains microtubules, actin micofil aments, and intermediate filaments. T hese collectively play a role in giving s hape to cells, allowing for cell moveme nt, movement of organelles within the cell and endocytosis, and cell division. Prokaryotic cell a. The ribosomes are composed of a 50 S and a 30S subunit forming an 70S ri bosome. b. Internal membrane-bound organell es such as mitochondria, endoplasmic reticulum, Golgi apparatus, vacuoles, and lysosomes are absent b. There are no chloroplasts. Photosyn thesis usually takes place in infoldings or extensions derived from the cytopla smic membrane. c. There is no mitosis and no mitotic s pindle. d. They may contains only actin-like p roteins that, along with the cell wall, c ontribute to cell shape.

15. 5. respiratory enzymes and electron transport chains eukaryotic cell - The electron transport syste m is located in the inner memb rane of the mitochondria prokaryotic cell - The electron transport syste m is located in the cytoplasmic membrane

16. 6. cell wall eukaryotic cell a. Plant cells, algae, and fungi have cell walls, usually compos ed of cellulose or chitin. Eukar yotic cell walls are never comp osed of peptidoglycan b. Animal cells and protozoans lack cell walls prokaryotic cell a. With few exceptions, memb ers of the domain Bacteria hav e cell walls composed of peptid oglycan b. Members of the domain Arc hae have cell walls composed o f protein, a complex carbohydr ate, or unique molecules resem bling but not the same as pepti doglycan.

17. 7. locomotor organelles eukaryotic cell - Eukaryotic cells may have fla gella or cilia. Flagella and cilia are organelles involved in loco motion and in eukaryotic cells consist of a distinct arrangeme nt of sliding microtubules surr ounded by a membrane. prokaryotic cell - Many prokaryotes have flagel la, each composed of a single, r otating fibril and usually not s urrounded by a membrane.

18. 8. representative organisms eukaryotic cell - The domain Eukarya: animal s, plants, algae, protozoans, an d fungi. prokaryotic cell - The domain Bacteria and the domain Archae. Since viruses are acellular and possess both living and nonliving characteristics, they are considered neither prokaryotic nor eukaryotic.

19. Learning Objectives for "Prokaryotic Cell Structure: The Cytoplasmic Membrane" 1. State the chemical composition and major function of the cytoplasmic membrane in bact eria. 2. Briefly describe the fluid phospholipid bilayer arrangement of biological membranes. 3. State the net flow of water when a cell is placed in an isotonic, hypertonic, or hypotonic e nvironment and relate this to the solute concentration. 4. Define the following means of transport: a. passive diffusion b. osmosis c. channel proteins d. uniporter e. antiporter f. symporter g. facilitated diffusion h. active transport i. the ABC transport system j. group translocation 5. State how the antibiotic polymyxin and disinfectants such as orthophenylphenol, chlorhe xidine, hexachlorophene, zephiran, and alcohol affect bacteria. 6. Define binary fission and geometric progression and relate this to bacteria being able to a stronomically increase their numbers in a relatively short period of time. 7. Briefly describe the process of binary fission in bacteria.

20. Plasmids and Transposons In addition to the nucleoid, many bacteria often contain small nonchromosomal DNA molecules called plasmids. Plasmids usually contain between 5 and 100 gen es. Plasmids are not essential for normal bacterial g rowth and bacteria may lose or gain them withou t harm.

21. They can, however, provide an advantage under certain environmental conditions. For exampl e, under normal environmental growth conditions, b acteria are not usually exposed to antibiotics and ha ving a plasmid coding for an enzyme capable of dena turing a particular antibiotic is of no value. However, if that bacterium finds itself in the body w hen the particular antibiotic that the plasmid-coded enzyme is able to degrade is being given to treat an i nfection, the bacterium containing the plasmid is abl e to survive and grow.

22. A. Structure and Composition Plasmids are small molecules of double strande d, helical, nonchromosomal DNA. Like the nucleoid, the two ends of the double-str anded DNA molecule that make up plasmids cov alently bond together forming a physical circle.

23. B. Functions Plasmids code for synthesis of a few proteins not c oded for by the nucleoid. For example, R-plasmids, found in some gram-negative bacteria, often have genes coding for both production of a conjugation pilus http://student.ccbcmd.edu/courses/bio141/lecguide/uni t1/prostruct/r.htmlhttp://student.ccbcmd.edu/courses/bio141/lecguide/uni t1/prostruct/r.html Through a process called conjugation, the conjugation pi lus enables the bacterium to transfer a copy of the R-plas mids to other bacteria, making them also multiple antibi otic resistant and able to produce a conjugation pilus.conjugation

24. C. Transposons (transposable elements or "ju mping genes") are small pieces of DNA that enco de enzymes that transpose the transposon, that i s, move it from one DNA location to anoth er. Transposons may be found as part of a bacte rium's nucleoid (conjugative transposons) or in plasmids and are usually between one and twe lve genes long.

25. Plasmids can also acquire a number of different antibiotic resistance genes by means of integrons. Integrons are transposons that can carry mul tiple gene clusters called gene cassettes th at move as a unit from one piece of DNA t o another. An enzyme called integrase enables these gene cassettes to integrate and accumulate within the integron. In this way, a number of diff erent antibiotic resistance genes can be transferr ed as a unit from one bacterium to another.

26. Plasmids and conjugative transposons are very i mportant in horizontal gene transfer in bacteria. Horizontal gene transfer, also known as late ral gene transfer, is a process in which an org anism transfers genetic material to anoth er cell that is not its offspring. The ability of Bacteria and Archaea to adapt to new environm ents as a part of bacterial evolution, most freque ntly results from the acquisition of new genes thr ough horizontal gene transfer rather than by the alteration of gene functions through mutations.

27. A transposon contains a number of genes, codin g for antibiotic resistance or other traits, flanked at both ends by insertion sequences coding for a n enzyme called transpoase.

28. Transpoase is the enzyme that catalyzes the cutti ng and resealing of the DNA during transpositio n. Thus, such transposons are able to cut themse lves out of a bacterial nucleoid or a plasmid and i nsert themselves into another nucleoid or plasmi d and contribute in the transmission of antibioti c resistance among a population of bacteria.

29. Biomolecules any organic molecule that is produced by a living organism, including large polymeric molecules s uch as proteins, polysaccharides, and nucleic aci ds as well as small molecules such as primary me tabolites, secondary metabolites, and natural pro ducts. A more general name for this class of mol ecules is a biogenic substance.organicmolecule organismpolymericproteinspolysaccharidesnucleic aci dssmall moleculesme tabolitessecondary metabolitesnatural pro ductsbiogenic substance

36. L-type amino acids present in nature Zwitterion:have both positive a nd negative charges

37. Carbohydrates are organic molecules with the general formula of CHO in 1:2:1 ratio. Although carbohydrates constitute only 1 to 2 percent of cell mass, they provide the raw fuel for cellular energy production. Carbohydrates are classified according to molecular size and solubility. In general, the smaller molecules are more soluble than the larger ones. Based on McMurry’s Organic Chemistry, 6 th edition

42. 42 Importance of Carbohydrates Distributed widely in nature Key intermediates of metabolism (sugars) Structural components of plants (cellulose) Central to materials of industrial products: pape r, lumber, fibers Key component of food sources: sugars, flour, ve getable fiber Contain OH groups on most carbons in linear ch ains or in rings

43. 43 Chemical Formula and Name Carbohydrates have roughly as many O’s as C’s (highly o xidized) Since H’s are about connected to each H and O the empi rical formulas are roughly (C(H 2 O)) n ▫Appears to be “carbon hydrate” from formula Current terminology: natural materials that contain ma ny hydroxyls and other oxygen-containing groups D+ Glucose C 6 H 12 O 6

44. 44 Sources Glucose is produced in plants through photosynt hesis from CO 2 and H 2 O Glucose is converted in plants to other small sug ars and polymers (cellulose, starch) Dietary carbohydrates provide the major source of energy required by organisms

45. 45 Classification of Carbohydrates Simple sugars (monosaccharides) can't be converted into smaller sugars by hydrolysis. Carbohydrates are made of two or more simple sugars co nnected as acetals (aldehyde and alcohol), oligosaccharid es and polysaccharides Sucrose (table sugar): disaccharide from two monosacch arides (glucose linked to fructose), Cellulose is a polysaccharide of several thousand glucose units connected by acetal linkages (aldehyde and alcohol)

46. 46 Aldoses and Ketoses aldo- and keto- prefixes identify the nature of the carb onyl group -ose suffix designates a carbohydrate Number of C’s in the monosaccharide indicated by roo t (-tri-, tetr-, pent-, hex-)

47. 47 The D -Sugar Family Correlation is always with D -(+)-glyceraldehyde (R) in C-I-P sense

48. 48 D, L Sugars Glyceraldehyde exists as two enantiomers, first identifi ed by their opposite rotation of plane polarized light Naturally occurring glyceraldehyde rotates plane-polar ized light in a clockwise direction, denoted (+) and is d esignated “(+)-glyceraldehyde” The enantiomer gives the opposite rotation and has a ( -) or “l” (levorotatory) prefix The direction of rotation of light does not correlate to any structural feature

49. 49 Cyclic Structures of Monosaccharides: Hemiacetal Formation Alcohols add reversibly to aldehydes and ketone s, forming hemiacetals

50. 50 Fischer Projection Structures of Anomers: All opyranose from Allose

51. 51 Glycosides Carbohydrate acetals are named by first citing th e alkyl group and then replacing the -ose ending of the sugar with –oside Stable in water, requiring acid for hydrolysis

52. 52 Disaccharides A disaccharide combines a hydroxyl of one mono saccharide in an acetal linkage with another A glycosidic bond between C1 of the first sugar (  or  ) and the  OH at C4 of the second sugar i s particularly common (a 1,4 link)

57. A growth medium or culture medium is a liquid or gel designed to support t he growth of microorganisms or cells [1], or small plants like the moss Physcomit rella patens [2]. There are different types of media for growing different types of c ells. [3]microorganismscells [1]plantsmossPhyscomit rella patens [2] [3] There are two major types of growth media: those used for cell culture, which us e specific cell types derived from plants or animals, and microbiological culture, which are used for growing microorganisms, such as bacteria or yeast. The most common growth media for microorganisms are nutrient broths and agar plates; specialized media are sometimes required for microorganism and cell culture gro wth. [1] Some organisms, termed fastidious organisms, require specialized enviro nments due to complex nutritional requirements. Viruses, for example, are oblig ate intracellular parasites and require a growth medium containing living cells.cell culturemicrobiological culturebacteriayeastagar plates [1]parasites

58. The chemical elements consumed in the greatest quantities by plants are carbon, hydrogen, and oxygen. These are present in the environment in the form of wate r and carbon dioxide; energy is provided by sunlight. Nitrogen, phosphorus, pota ssium, and sulfur are also needed in relatively large quantities. Together, these a re the elemental macronutrients for plants, often represented by the acronym CHNOPS. Usually they are sourced from inorganic (e.g. carbon dioxide, water, ni trate, phosphate, sulfate) or organic (e.g. carbohydrates, lipids, proteins) compo unds, although elemental diatomic molecules of nitrogen and (especially) oxygen are often used.carbon hydrogenoxygenwate rcarbon dioxidesunlightNitrogenphosphoruspota ssiumsulfuracronymcarbon dioxidewaterni tratephosphatesulfatecarbohydrateslipidsproteinscompo undsdiatomic molecules macronutrients

59. 유기화합물 : 탄소공급원 CO2: 탄소공급원 Chemo- : 무기화합물의 산화 : 에너지 공급원 Photo-: 빛 : 에너지 공급원

61. C. HOPKiN'S CaFe Mg (to be used as C. Hopkins coffee mug) : carbon, hydro gen, oxygen, phosphorus, potassium, nitrogen, sulfur, calcium, iron, and ma gnesium.potassiumsulfurcalciumironma gnesium

62. micronutrients micronutrients because they are needed only in minuscule amounts, th ese substances are the “magic wands” that enable the body to produce enzymes, hormones and other substances essential for proper growth a nd development. As tiny as the amounts are, however, the consequences of their absenc e are severe. Iodine, vitamin A and iron are most important in global public health t erms; their lack represents a major threat to the health and developme nt of populations the world over, particularly children and pregnant w omen in low-income countries.